@misc{HoffmannSchultzSchellhornetal.2014, author = {Hoffmann, Ren{\´e} and Schultz, Julia A. and Schellhorn, Rico and Rybacki, Erik and Keupp, Helmut and Lemanis, Robert and Zachow, Stefan}, title = {Non-invasive imaging methods applied to neo- and paleo-ontological cephalopod research}, issn = {1438-0064}, doi = {10.5194/bg-11-2721-2014}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-50300}, year = {2014}, abstract = {Several non-invasive methods are common practice in natural sciences today. Here we present how they can be applied and contribute to current topics in cephalopod (paleo-) biology. Different methods will be compared in terms of time necessary to acquire the data, amount of data, accuracy/resolution, minimum/maximum size of objects that can be studied, the degree of post-processing needed and availability. The main application of the methods is seen in morphometry and volumetry of cephalopod shells. In particular we present a method for precise buoyancy calculation. Therefore, cephalopod shells were scanned together with different reference bodies, an approach developed in medical sciences. It is necessary to know the volume of the reference bodies, which should have similar absorption properties like the object of interest. Exact volumes can be obtained from surface scanning. Depending on the dimensions of the study object different computed tomography techniques were applied.}, language = {en} } @misc{EhlkeFrenzelRammetal.2014, author = {Ehlke, Moritz and Frenzel, Thomas and Ramm, Heiko and Lamecker, Hans and Akbari Shandiz, Mohsen and Anglin, Carolyn and Zachow, Stefan}, title = {Robust Measurement of Natural Acetabular Orientation from AP Radiographs using Articulated 3D Shape and Intensity Models}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-49824}, year = {2014}, language = {en} } @misc{LamasRodriguezEhlkeHoffmannetal.2015, author = {Lamas-Rodr{\´i}guez, Juli{\´a}n and Ehlke, Moritz and Hoffmann, Ren{\´e} and Zachow, Stefan}, title = {GPU-accelerated denoising of large tomographic data sets with low SNR}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-56339}, year = {2015}, abstract = {Enhancements in tomographic imaging techniques facilitate non-destructive methods for visualizing fossil structures. However, to penetrate dense materials such as sediments or pyrites, image acquisition is typically performed with high beam energy and very sensitive image intensifiers, leading to artifacts and noise in the acquired data. The analysis of delicate fossil structures requires the images to be captured in maximum resolution, resulting in large data sets of several giga bytes (GB) in size. Since the structural information of interest is often almost in the same spatial range as artifacts and noise, image processing and segmentation algorithms have to cope with a very low signal-to-noise ratio (SNR). Within this report we present a study on the performance of a collection of denoising algorithms applied to a very noisy fossil dataset. The study shows that a non-local means (NLM) filter, in case it is properly configured, is able to remove a considerable amount of noise while preserving most of the structural information of interest. Based on the results of this study, we developed a software tool within ZIBAmira that denoises large tomographic datasets using an adaptive, GPU-accelerated NLM filter. With the help of our implementation a user can interactively configure the filter's parameters and thus its effectiveness with respect to the data of interest, while the filtering response is instantly visualized for a preselected region of interest (ROI). Our implementation efficiently denoises even large fossil datasets in a reasonable amount of time.}, language = {en} } @misc{JoachimskyAmbellanZachow2017, author = {Joachimsky, Robert and Ambellan, Felix and Zachow, Stefan}, title = {Computerassistierte Auswahl und Platzierung von interpositionalen Spacern zur Behandlung fr{\"u}her Gonarthrose}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66064}, year = {2017}, abstract = {Degenerative Gelenkerkrankungen, wie die Osteoarthrose, sind ein h{\"a}ufiges Krankheitsbild unter {\"a}lteren Erwachsenen. Hierbei verringert sich u.a. der Gelenkspalt aufgrund degenerierten Knorpels oder gesch{\"a}digter Menisci. Ein in den Gelenkspalt eingebrachter interpositionaler Spacer soll die mit der Osteoarthrose einhergehende verringerte Gelenkkontaktfl{\"a}che erh{\"o}hen und so der teilweise oder vollst{\"a}ndige Gelenkersatz hinausgez{\"o}gert oder vermieden werden. In dieser Arbeit pr{\"a}sentieren wir eine Planungssoftware f{\"u}r die Auswahl und Positionierung eines interpositionalen Spacers am Patientenmodell. Auf einer MRT-basierten Bildsegmentierung aufbauend erfolgt eine geometrische Rekonstruktion der 3D-Anatomie des Kniegelenks. Anhand dieser wird der Gelenkspalt bestimmt, sowie ein Spacer ausgew{\"a}hlt und algorithmisch vorpositioniert. Die Positionierung des Spacers ist durch den Benutzer jederzeit interaktiv anpassbar. F{\"u}r jede Positionierung eines Spacers wird ein Fitness-Wert zur Knieanatomie des jeweiligen Patienten berechnet und den Nutzern R{\"u}ckmeldung hinsichtlich Passgenauigkeit gegeben. Die Software unterst{\"u}tzt somit als Entscheidungshilfe die behandelnden {\"A}rzte bei der patientenspezifischen Spacerauswahl.}, language = {de} } @misc{HegeMerzkyZachow2000, author = {Hege, Hans-Christian and Merzky, Andre and Zachow, Stefan}, title = {Distributed Visualization with OpenGL Vizserver: Practical Experiences}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-5992}, number = {00-31}, year = {2000}, abstract = {The increasing demand for distributed solutions in computing technology does not stop when it comes to visualization techniques. However, the capabilities of todays applications to perform remote rendering are limited by historical design legacys. Especially the popular X11 protokoll, which has been proven to be extremely flexible and usefull for remote 2D graphics applications, breaks down for the case of remote 3D rendering. In this white paper, we give a short overview of generic remote rendering technologies available today, and compare their performance to the recently released vizserver by SGI: a network extension to the SGI OpenGL rendering engines.}, language = {en} } @misc{KoberSaderZeilhoferetal.2001, author = {Kober, Cornelia and Sader, Robert and Zeilhofer, Hans-Florian and Prohaska, Steffen and Zachow, Stefan and Deuflhard, Peter}, title = {Anisotrope Materialmodellierung f{\"u}r den menschlichen Unterkiefer}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-6574}, number = {01-31}, year = {2001}, abstract = {Im Rahmen der biomechanischen Simulation kn{\"o}cherner Organe ist die Frage nach einer befriedigenden Materialbeschreibung nach wie vor ungel{\"o}st. Computertomographische Datens{\"a}tze liefern eine r{\"a}umliche Verteilung der (R{\"o}ntgen-)Dichte und erm{\"o}glichen damit eine gute Darstellung der individuellen Geometrie. Weiter k{\"o}nnen die verschiedenen Materialbestandteile des Knochens, Spongiosa und Kortikalis, voneinander getrennt werden. Aber die richtungsab{\"a}ngige Information der Materialanisotropie ist verloren. In dieser Arbeit wird ein Ansatz f{\"u}r eine anisotrope Materialbeschreibung vorgestellt, die es erm{\"o}glicht, den Einfluss der individuellen kn{\"o}chernen Struktur auf das makroskopische Materialverhalten abzusch{\"a}tzen.}, language = {de} } @misc{ZachowZilskeHege2007, author = {Zachow, Stefan and Zilske, Michael and Hege, Hans-Christian}, title = {3D reconstruction of individual anatomy from medical image data: Segmentation and geometry processing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-10440}, number = {07-41}, year = {2007}, abstract = {For medical diagnosis, visualization, and model-based therapy planning three-dimensional geometric reconstructions of individual anatomical structures are often indispensable. Computer-assisted, model-based planning procedures typically cover specific modifications of "virtual anatomy" as well as numeric simulations of associated phenomena, like e.g. mechanical loads, fluid dynamics, or diffusion processes, in order to evaluate a potential therapeutic outcome. Since internal anatomical structures cannot be measured optically or mechanically in vivo, three-dimensional reconstruction of tomographic image data remains the method of choice. In this work the process chain of individual anatomy reconstruction is described which consists of segmentation of medical image data, geometrical reconstruction of all relevant tissue interfaces, up to the generation of geometric approximations (boundary surfaces and volumetric meshes) of three-dimensional anatomy being suited for finite element analysis. All results presented herein are generated with amira ® - a highly interactive software system for 3D data analysis, visualization and geometry reconstruction.}, language = {en} } @misc{TackShestakovLuedkeetal.2021, author = {Tack, Alexander and Shestakov, Alexey and L{\"u}dke, David and Zachow, Stefan}, title = {A deep multi-task learning method for detection of meniscal tears in MRI data from the Osteoarthritis Initiative database}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-84415}, year = {2021}, abstract = {We present a novel and computationally efficient method for the detection of meniscal tears in Magnetic Resonance Imaging (MRI) data. Our method is based on a Convolutional Neural Network (CNN) that operates on a complete 3D MRI scan. Our approach detects the presence of meniscal tears in three anatomical sub-regions (anterior horn, meniscal body, posterior horn) for both the Medial Meniscus (MM) and the Lateral Meniscus (LM) individually. For optimal performance of our method, we investigate how to preprocess the MRI data or how to train the CNN such that only relevant information within a Region of Interest (RoI) of the data volume is taken into account for meniscal tear detection. We propose meniscal tear detection combined with a bounding box regressor in a multi-task deep learning framework to let the CNN implicitly consider the corresponding RoIs of the menisci. We evaluate the accuracy of our CNN-based meniscal tear detection approach on 2,399 Double Echo Steady-State (DESS) MRI scans from the Osteoarthritis Initiative database. In addition, to show that our method is capable of generalizing to other MRI sequences, we also adapt our model to Intermediate-Weighted Turbo Spin-Echo (IW TSE) MRI scans. To judge the quality of our approaches, Receiver Operating Characteristic (ROC) curves and Area Under the Curve (AUC) values are evaluated for both MRI sequences. For the detection of tears in DESS MRI, our method reaches AUC values of 0.94, 0.93, 0.93 (anterior horn, body, posterior horn) in MM and 0.96, 0.94, 0.91 in LM. For the detection of tears in IW TSE MRI data, our method yields AUC values of 0.84, 0.88, 0.86 in MM and 0.95, 0.91, 0.90 in LM. In conclusion, the presented method achieves high accuracy for detecting meniscal tears in both DESS and IW TSE MRI data. Furthermore, our method can be easily trained and applied to other MRI sequences.}, language = {en} } @misc{AmbellanZachowvonTycowicz2021, author = {Ambellan, Felix and Zachow, Stefan and von Tycowicz, Christoph}, title = {Geodesic B-Score for Improved Assessment of Knee Osteoarthritis}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-81930}, year = {2021}, abstract = {Three-dimensional medical imaging enables detailed understanding of osteoarthritis structural status. However, there remains a vast need for automatic, thus, reader-independent measures that provide reliable assessment of subject-specific clinical outcomes. To this end, we derive a consistent generalization of the recently proposed B-score to Riemannian shape spaces. We further present an algorithmic treatment yielding simple, yet efficient computations allowing for analysis of large shape populations with several thousand samples. Our intrinsic formulation exhibits improved discrimination ability over its Euclidean counterpart, which we demonstrate for predictive validity on assessing risks of total knee replacement. This result highlights the potential of the geodesic B-score to enable improved personalized assessment and stratification for interventions.}, language = {en} }